Integrated multi-omics unravels bioactive metabolic networks during red chicory heading

Red chicory (Cichorium intybus L.) is a leafy vegetable rich in bioactive compounds; however, the metabolic mechanisms underlying its nutritional quality during heading remain poorly understood. A comparison of basic nutritional components across ten inbred lines identified LC018 as exhibiting superior nutrient accumulation. The metabolomics analysis detected 1471 metabolites, including 367 flavonoids, 230 phenolic acids, 152 lipids, 132 terpenoids, and 590 other compounds. Of these, 571 differentially accumulated metabolites displayed stage-specific changes throughout leafy head development. Transcriptomic analysis revealed 5830 differentially expressed genes significantly enriched in secondary metabolite biosynthesis pathways. Integrated multi-omics analysis identified key structural genes and transcription factors strongly associated with metabolite accumulation, highlighting their involvement in the biosynthesis of flavonoids, phenolic acids, lipids, and sesquiterpenes. These findings provide key insights into the molecular basis of nutritional quality in red chicory during heading and identify genetic targets for developing high-value cultivars with increased bioactive compound content.